Origin of yaws in the Pleistocene

Technical note: The use and misuse of threshold diagnostic criteria in paleopathology

Weighted threshold diagnostic criteria approaches have emerged for diseases that involve skeletal/bony tissue that are readily diagnosed in the field of paleopathology such as Vitamin C deficiency (scurvy), Vitamin D deficiency (rickets) and treponemal disease. These criteria differ from traditional differential diagnosis in that they involve standardized inclusion criteria based on the lesion's specificity to the disease. Here I discuss the limitations and benefits of threshold criteria. I argue that while these criteria will benefit from further revision such as inclusion of lesion severity, and the incorporation of exclusion criteria, threshold diagnostic approaches have considerable value in the future of diagnosis in the field.

The taxonomic attribution of African hominin postcrania from the Miocene through the Pleistocene: Associations and assumptions

Postcranial bones may provide valuable information about fossil taxa relating to their locomotor habits, manipulative abilities and body sizes. Distinctive features of the postcranial skeleton are sometimes noted in species diagnoses. Although numerous isolated postcranial fossils have become accepted by many workers as belonging to a particular species, it is worthwhile revisiting the evidence for each attribution before including them in comparative samples in relation to the descriptions of new fossils, functional analyses in relation to particular taxa, or in evolutionary contexts. Although some workers eschew the taxonomic attribution of postcranial fossils as being less important (or interesting) than interpreting their functional morphology, it is impossible to consider the evolution of functional anatomy in a taxonomic and phylogenetic vacuum. There are 21 widely recognized hominin taxa that have been described from sites in Africa dated from the Late Miocene to the Middle Pleistocene; postcranial elements have been attributed to 17 of these. The bones that have been thus assigned range from many parts of a skeleton to isolated elements. However, the extent to which postcranial material can be reliably attributed to a specific taxon varies considerably from site to site and species to species, and is often the subject of considerable debate. Here, we review the postcranial remains attributed to African hominin taxa from the Late Miocene to the Middle and Late Pleistocene and place these assignations into categories of reliability. The catalog of attributions presented here may serve as a guide for making taxonomic decisions in the future.

Advancing the understanding of treponemal disease in the past and present

Syphilis was perceived to be a new disease in Europe in the late 15th century, igniting a debate about its origin that continues today in anthropological, historical, and medical circles. We move beyond this age-old debate using an interdisciplinary approach that tackles broader questions to advance the understanding of treponemal infection (syphilis, yaws, bejel, and pinta). How did the causative organism(s) and humans co-evolve? How did the related diseases caused by Treponema pallidum emerge in different parts of the world and affect people across both time and space? How are T. pallidum subspecies related to the treponeme causing pinta? The current state of scholarship in specific areas is reviewed with recommendations made to stimulate future work. Understanding treponemal biology, genetic relationships, epidemiology, and clinical manifestations is crucial for vaccine development today and for investigating the distribution of infection in both modern and past populations. Paleopathologists must improve diagnostic criteria and use a standard approach for recording skeletal lesions on archaeological human remains. Adequate contextualization of cultural and environmental conditions is necessary, including site dating and justification for any corrections made for marine or freshwater reservoir effects. Biogeochemical analyses may assess aquatic contributions to diet, physiological changes arising from treponemal disease and its treatments (e.g., mercury), or residential mobility of those affected. Shifting the focus from point of origin to investigating who is affected (e.g., by age/sex or socioeconomic status) and disease distribution (e.g., coastal/ inland, rural/urban) will advance our understanding of the treponemal disease and its impact on people through time.

Ancient pathogen genomics: insights into timing and adaptation

Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.

Neurosyphilis

No portion of the central nervous system is immune to the ravages of syphilis. Infection by Treponema pallidum can affect the meninges, brain, brainstem, spinal cord, nerve roots, and cerebral and spinal blood vessels. As a consequence, the disease may present in diverse and, at times, diagnostically challenging fashions. Neurologic manifestations of syphilis may develop within months of the initial infection or, alternatively, take decades to appear. Although approximately one-third of individuals infected by T. pallidum display cerebrospinal fluid abnormalities suggestive of invasion of the central nervous system by the organism, only a fraction of these develop clinically significant neurologic manifestations. The features of neurosyphilis may be modified by the concomitant presence of immunosuppressive agents or conditions such as HIV/AIDS. The epidemiology of neurosyphilis has largely paralleled that of syphilis in general. A dramatic decline occurred by the early 1950s as a consequence of public health measures and the widespread use of antibiotics. The incidence had increased by the onset of the AIDS pandemic and has since corresponded with the adoption of safe sex practices. The CSF Venereal Disease Research Laboratory (VDRL) test remains the "gold standard" for diagnosis, but is not invariably positive. Penicillin remains the most effective and recommended therapy.

The endemic treponematoses

The agents of human treponematoses include four closely related members of the genus Treponema: three subspecies of Treponema pallidum plus Treponema carateum. T. pallidum subsp. pallidum causes venereal syphilis, while T. pallidum subsp. pertenue, T. pallidum subsp. endemicum, and T. carateum are the agents of the endemic treponematoses yaws, bejel (or endemic syphilis), and pinta, respectively. All human treponematoses share remarkable similarities in pathogenesis and clinical manifestations, consistent with the high genetic and antigenic relatedness of their etiological agents. Distinctive features have been identified in terms of age of acquisition, most common mode of transmission, and capacity for invasion of the central nervous system and fetus, although the accuracy of these purported differences is debated among investigators and no biological basis for these differences has been identified to date. In 2012, the World Health Organization (WHO) officially set a goal for yaws eradication by 2020. This challenging but potentially feasible endeavor is favored by the adoption of oral azithromycin for mass treatment and the currently focused distribution of yaws and endemic treponematoses and has revived global interest in these fascinating diseases and their causative agents.

Genomics, the origins of agriculture, and our changing microbe-scape: time to revisit some old tales and tell some new ones

Though agriculture is often viewed as one of humanity's crowning achievements, skeletal evidence indicates that dependence on domesticated plants and animals was accompanied by an increase in infectious disease. Scientists have proposed that many important infections emerged in the period following the advent of agriculture, as a result of newly dense populations and novel proximity to domestic animals that served as reservoirs for novel pathogens. Here, we review genomic evidence regarding pathogen origins, analyzing these data using the epidemiological transition framework. Genetic information has forced us to reconsider how and when many important pathogens emerged; it appears that a number of infections thought to result from contact with domesticated animals arose much earlier than agriculture was adopted. We also consider the broader effect of agriculture upon the microbiome, exploring potential consequences for human health. We end by discussing the changes in the human microbe-scape we are likely to see in the future.

Whole genome sequence of the Treponema Fribourg-Blanc: unspecified simian isolate is highly similar to the yaws subspecies

Background

Unclassified simian strain Treponema Fribourg-Blanc was isolated in 1966 from baboons (Papio cynocephalus) in West Africa. This strain was morphologically indistinguishable from T. pallidum ssp. pallidum or ssp. pertenue strains, and it was shown to cause human infections.

Methodology/Principal Findings

To precisely define genetic differences between Treponema Fribourg-Blanc (unclassified simian isolate, FB) and T. pallidum ssp. pertenue strains (TPE), a high quality sequence of the whole Fribourg-Blanc genome was determined with 454-pyrosequencing and Illumina sequencing platforms. Combined average coverage of both methods was greater than 500×. Restriction target sites (n = 1,773), identified in silico, of selected restriction enzymes within the Fribourg-Blanc genome were verified experimentally and no discrepancies were found. When compared to the other three sequenced TPE genomes (Samoa D, CDC-2, Gauthier), no major genome rearrangements were found. The Fribourg-Blanc genome clustered with other TPE strains (especially with the TPE CDC-2 strain), while T. pallidum ssp. pallidum strains clustered separately as well as the genome of T. paraluiscuniculi strain Cuniculi A. Within coding regions, 6 deletions, 5 insertions and 117 substitutions differentiated Fribourg-Blanc from other TPE genomes.

Conclusions/Significance

The Fribourg-Blanc genome showed similar genetic characteristics as other TPE strains. Therefore, we propose to rename the unclassified simian isolate to Treponema pallidum ssp. pertenue strain Fribourg-Blanc. Since the Fribourg-Blanc strain was shown to cause experimental infection in human hosts, non-human primates could serve as possible reservoirs of TPE strains. This could considerably complicate recent efforts to eradicate yaws. Genetic differences specific for Fribourg-Blanc could then contribute for identification of cases of animal-derived yaws infections.

A bacterial strain isolated in 1966 from baboons (Papio cynocephalus) in West Africa was preliminarily characterized as unclassified simian strain Treponema Fribourg-Blanc (FB). This strain was morphologically identical to T. pallidum ssp. pallidum (TPA, agent of syphilis) or ssp. pertenue (TPE, agent of yaws). In this study, we completed a high quality whole genome sequence of simian isolate Treponema Fribourg-Blanc and compared it to known genome sequences of Treponema pallidum strains. No major differences in the gene order of the FB genome were found when compared to all known genomes of Treponema pallidum subspecies. Moreover, the FB genome clustered with other TPE strains, while T. pallidum ssp. pallidum strains clustered separately. In general, the FB genome showed similar genetic characteristics to other TPE strains. Therefore, we proposed that the simian isolate Fribourg-Blanc be classified as a bacterial strain belonging to Treponema pallidum ssp. pertenue. It appears that, except for humans, the reservoir of yaws-causing treponemes may also include free-living primates, especially in Africa.

Yaws

Yaws is an infectious disease caused by Treponema pallidum pertenue-a bacterium that closely resembles the causative agent of syphilis-and is spread by skin-to-skin contact in humid tropical regions. Yaws causes disfiguring, and sometimes painful lesions of the skin and bones. As with syphilis, clinical manifestations can be divided into three stages; however, unlike syphilis, mother-to-child transmission does not occur. A major campaign to eradicate yaws in the 1950s and 1960s, by mass treatment of affected communities with longacting, injectable penicillin, reduced the number of cases by 95% worldwide, but yaws has reappeared in recent years in Africa, Asia, and the western Pacific. In 2012, one oral dose of azithromycin was shown to be as effective as intramuscular penicillin in the treatment of the disease, and WHO launched a new initiative to eradicate yaws by 2020.

Earliest porotic hyperostosis on a 1.5-million-year-old hominin, olduvai gorge, Tanzania

Meat-eating was an important factor affecting early hominin brain expansion, social organization and geographic movement. Stone tool butchery marks on ungulate fossils in several African archaeological assemblages demonstrate a significant level of carnivory by Pleistocene hominins, but the discovery at Olduvai Gorge of a child's pathological cranial fragments indicates that some hominins probably experienced scarcity of animal foods during various stages of their life histories. The child's parietal fragments, excavated from 1.5-million-year-old sediments, show porotic hyperostosis, a pathology associated with anemia. Nutritional deficiencies, including anemia, are most common at weaning, when children lose passive immunity received through their mothers' milk. Our results suggest, alternatively, that (1) the developmentally disruptive potential of weaning reached far beyond sedentary Holocene food-producing societies and into the early Pleistocene, or that (2) a hominin mother's meat-deficient diet negatively altered the nutritional content of her breast milk to the extent that her nursing child ultimately died from malnourishment. Either way, this discovery highlights that by at least 1.5 million years ago early human physiology was already adapted to a diet that included the regular consumption of meat.

Syphilis at the crossroad of phylogenetics and paleopathology

The origin of syphilis is still controversial. Different research avenues explore its fascinating history. Here we employed a new integrative approach, where paleopathology and molecular analyses are combined. As an exercise to test the validity of this approach we examined different hypotheses on the origin of syphilis and other human diseases caused by treponemes (treponematoses). Initially, we constructed a worldwide map containing all accessible reports on palaeopathological evidences of treponematoses before Columbus's return to Europe. Then, we selected the oldest ones to calibrate the time of the most recent common ancestor of Treponema pallidum subsp. pallidum, T. pallidum subsp. endemicum and T. pallidum subsp. pertenue in phylogenetic analyses with 21 genetic regions of different T. pallidum strains previously reported. Finally, we estimated the treponemes' evolutionary rate to test three scenarios: A) if treponematoses accompanied human evolution since Homo erectus; B) if venereal syphilis arose very recently from less virulent strains caught in the New World about 500 years ago, and C) if it emerged in the Americas between 16,500 and 5,000 years ago. Two of the resulting evolutionary rates were unlikely and do not explain the existent osseous evidence. Thus, treponematoses, as we know them today, did not emerge with H. erectus, nor did venereal syphilis appear only five centuries ago. However, considering 16,500 years before present (yBP) as the time of the first colonization of the Americas, and approximately 5,000 yBP as the oldest probable evidence of venereal syphilis in the world, we could not entirely reject hypothesis C. We confirm that syphilis seems to have emerged in this time span, since the resulting evolutionary rate is compatible with those observed in other bacteria. In contrast, if the claims of precolumbian venereal syphilis outside the Americas are taken into account, the place of origin remains unsolved. Finally, the endeavor of joining paleopathology and phylogenetics proved to be a fruitful and promising approach for the study of infectious diseases.

Syphilis is a reemerging disease burden. Although it has been studied for five centuries, its origin and spread is still controversial. Did it accompany the evolution of the genus Homo and does it date back to more than a million years or did it emerge only after Columbus's return to Europe? Initially, to test the validity of a new interdisciplinary approach we constructed a worldwide map showing precolumbian human skeletons with lesions of syphilis and other related diseases (also caused by different treponemes). Then, we selected the oldest cases to estimate the timing of the treponemes' history, using their DNA sequences and computer simulations. This resulted in treponeme evolutionary rates, and in temporal intervals during which these microorganisms could have emerged. Based on comparisons with other bacteria, we concluded that treponematoses did not emerge before our own species originated and that syphilis did not start affecting mankind only from 1492 onwards. Instead, it seems to have emerged in the time span between 16,500 and 5,000 years ago. Where syphilis emerged, however, remains unsolved. Finally, the endeavor of joining as distinct fields as paleopathology and molecular biology proved to be fruitful and promising to advance our understanding of the rise and fall of the infectious diseases that have afflicted humans across time and space.

Climate and New World periosteal reaction patterns: implications for migration routes into the western hemisphere

The presence of the diseases yaws and bejel are indicated by periosteal reaction patterns. The distributions of these two diseases in ancient North American human populations show evidence of climatic influence. Those ancient populations lacking either yaws or bejel (the null periosteal reaction pattern) can be found in the coldest parts of the Cold Winter Regions. Those populations with yaws (the poly-ostotic periosteal reaction) can be found in the milder portions of the Cold Winter Regions. The populations with bejel (the pauci-ostotic periosteal reaction) are found either outside of or marginal to Cold Winter Regions. The Bering Strait area is considered to be the gateway to the ancient New World. The cold climates present in this area should have influenced the routes available for the diseases to spread from population to population or by migration of infected populations into the Western Hemisphere. It is suggested that the coastal route with its milder maritime climate was the route taken by yaws when it entered the New World. The presence of bejel in ancient North America presents a conundrum. The climate would have blocked the spread of the disease from Siberia to Alaska in either Late Glacial or Holocene times. This suggests that our present view of migration routes is incomplete.

Body proportions of Homo habilis reviewed

The ratio of fore- to hindlimb size plays an important role in our understanding of human evolution. Although Homo habilis was relatively modern craniodentally, its body proportions are commonly believed to have been more apelike than in the earlier Australopithecus afarensis. The evidence for this, however, rests, on two fragmentary skeletons, OH 62 and KNM-ER 3735. The upper limb of the better-preserved OH 62 from Olduvai Gorge is long and slender, but its hindlimb is represented mainly by the proximal portion of a thin femur of uncertain length. The present analysis shows that upper-to-lower limb shaft proportions of both OH 62 and AL 288-1 (A. afarensis) fall in the modern human range of variation, although OH 62 also falls inside that of chimpanzees due to their overlap in small individuals. Despite being more fragmentary, the larger-bodied KNM-ER 3735 lies outside the chimpanzee range and close to the human mean. Because the differences between any of the three individuals are compatible with the range of variation seen in extant hominoid groups, it is not legitimate to infer more primitive upper-to-lower limb shaft proportions for either H. habilis or A. afarensis. Femur length of OH 62 can only be estimated by comparison. Its closest match in size and morphology is with the gracile OH 34 specimen, which therefore provides a better analogue for the reconstruction of OH 62 than the stocky AL 288-1 femur that is traditionally used. OH 34's slender proportions are hardly due to abrasion, but match those of a modern human of that body-size, suggesting that the relative length of OH 62's leg may have been human-like. Brachial proportions, however, remained primitive. Long legs may imply long distance terrestrial travel. Perhaps this adaptation evolved early in the genus Homo, with H. habilis providing an early representative of this important change.

Community participation eliminates yaws in Ecuador

Yaws is no longer a national and international health priority for intervention, but there is still a negative perception of the disease in the few affected communities. A survey in 1988 in the northern region of Ecuador documented a prevalence of 16.5% of clinical cases and 96.3% of serological cases. A continuous, long-term community-based surveillance programme was therefore put in place focusing on yaws as one of the sentinel diseases. The results of this intervention are reported here. In 1993, a second survey showed a reduction in the prevalence of clinical cases to 1.4% and of serological cases to 4.7%. Between 1993 and 1998, no other clinical cases were detected and the serological prevalence in 1998 was 3.5%, corresponding with clinical cases of primary or congenital syphilis, latent yaws under follow-up, and individuals with low serological titres indicating a 'serological scar'. These data indicate that yaws has been eliminated. Another important outcome of the intervention is the increased self-confidence in the communities that health problems can be tackled.

Syphilis 2001--a palaeopathological reappraisal

The origin and subsequent spread of the treponematoses, especially that of venereal syphilis, has been the subject of considerable scientific attention. Various theories were put forth and palaeopathological specimens were used for their validation in recent times. One influential contribution was the paper by Baker & Armelagos in 1988. Numerous new findings and results on both sides of the Atlantic call for a new evaluation of the available osseous material. A review of the recent literature leads to the suggestion of a worldwide distribution of non-venereal treponemal disease since the emergence of Homo and to a first epidemic outbreak of venereal syphilis in Europe of the late 15th and the early 16th century, which was a time of change and enormous sexual liberty. Old World specimens with pathological alterations attributed to venereal syphilis and dated to precolumbian times seem to invalidate the Columbian theory and call for a more differentiated analysis of the phenomenon of syphilis than a theory based on a single factor can provide. With the help of molecular methods which now allow a positive identification of Treponema pallidum pallidum, causative agent of venereal syphilis, in palaeopathological material, it seems possible to elucidate the matter of origin and spread of syphilis further and to evaluate previous diagnoses of treponemal disease.

Axial and appendicular skeleton of Homo antecessor

The human trunk and limb bones recovered from the Gran Dolina site, in the Sierra de Atapuerca (Burgos, Spain) are studied. All these fossils were excavated at the level called TD6 between 1994 and 1995 and have been dated in excess of 780,000 years ago. These remains have been recently attributed to a new Homo species named Homo antecessor. Axial (vertebrae and ribs) and part of the appendicular (clavicles, radii, femur and patellae) skeleton are studied here. Hand and foot bones have been studied elsewhere (Lorenzo et al., 1999). Four is the minimum number of individuals represented by the postcranial remains recovered up to now. All elements are briefly described anatomically, measured and compared with other fossil hominids and modern humans in order to establish, as far as possible, what postcranial morphology characterized this new species of our genus. The H. antecessor postcrania, generally, display a set of morphological traits that are more similar to modern humans than to the Middle and Upper Pleistocene European hominids. Our results do not contradict the previous phylogenetic analysis, i.e., that H. antecessor represents the last common ancestor for H. sapiens (modern humans) and H. neanderthalensis (Neandertals).

Clavicles, scapulae and humeri from the Sima de los Huesos site (Sierra de Atapuerca, Spain)

The scapulae, clavicles and humeri recovered from the Sima de los Huesos (SH) site between 1976 and 1994 are studied. All elements are briefly described anatomically with metrics and compared with other fossil hominids in order to establish the morphological pattern of the SH hominids. A minimum of 13 individuals are represented by the humeri in the SH sample. Almost all of them can be classified as adolescents and young adults. The morphology of the SH hominid shoulder girdle and humeri indicates that much of the shoulder morphology recognized in the later true Neandertal was present in Europe long before they appeared. Thus, this morphological pattern is not exclusive to Neandertals alone. The SH clavicles, scapulae and humeri share with the Neandertals many traits usually considered to be Neandertal specializations. The comparative analysis of the SH evidence suggests that most of the SH and Neandertal shared traits are either primitive features within the genus Homo or even for all hominids, or display high variability within different hominid samples. These traits must be used with caution, or not used at all, in phylogenetic analysis. There are, however, traits that to date have only been detected in the SH hominids and the Neanderials, which could be exclusive to the European phyletic lineage (clade) of Homo.

Paleopathological evidence of the cranial remains from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain). Description and preliminary inferences

The large Sima de los Huesos sample provides for the first time the opportunity of performing a paleopathological study of a Middle Pleistocene population. A high frequency of bilateral temporomandibular arthropathy has been observed. We found an ear hyperostosis in Cranium 4, that probably caused deafness that we consider to be of infectious origin. Three osteomata were found in the cranial collection. One severe trauma was evident on the left supraorbital torus of an immature individual. Many cranial vault erosions, mostly restricted to the external table, are found in the sample. Cranium 5 displays thirteen of these. Cranium 5 also shows an extensive maxillary osteitis associated with a dental apical abscess, as well as another dental apical abscess in its mandible. Most of the adult frontal bones show a worm-like pattern of vascular channelling in the orbital roof, also found in modern populations.

Endocranial hyperostosis in Sangiran 2, Gibraltar 1, and Shanidar 5

Sangiran hominid 2 (S-2), Gibraltar hominid 1 (G-1), and Shanidar hominid 5 (SH-5) exhibit previously undescribed bilateral, paramedian hyperostosis of the endocranial frontal squama that spares the frontal crest, sagittal sinus, and ectocranial surface. The hyperostosis is localized to the frontal (usually the middle third) and parietal and is consistent with a diagnosis of hyperostosis calvaria interna (HCI), inclusive of hyperostosis frontalis interna. The hyperostosis in these specimens is compared to fossil hominids from Indonesia and Europe and to modern human cases of HCI. The three cases of HCI reported here documented the existence and frequency of HCI in fossil hominids and push the antiquity of the disease back to nearly 1.5 million years. The relatively great incidence of HCI in fossil hominids adds another confounding factor to the problematical issue of the taxonomic significance of cranial vault thickness.